NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P45520 UniProt NPD GO	ACT_LEIMA	Actin	0.00	-	cyt	0	Cytoplasm				376
P53477 UniProt NPD GO	ACT_TRYCR	Actin	0.00	-	cyt	0	Cytoplasm				376
Q39596 UniProt NPD GO	ACT_CHERU	Actin (Fragment)	0.00	-	nuc	0	Cytoplasm				85
Q11212 UniProt NPD GO	ACT_SPOLI	Actin (Fragment)	0.00	-	cyt	0	Cytoplasm				164
P81085 UniProt NPD GO	ACT_PINPS	Actin (Water stress-responsive protein 5) (Fragment)	0.00	-		0	Cytoplasm (By similarity)				15
P12433 UniProt NPD GO	ACT2_TRYBB	Actin B	0.00	-	cyt	0	Cytoplasm				376
P02581 UniProt NPD GO	ACT1_SOYBN	Actin-1	0.00	-	mit	1	Cytoplasm				377
P10982 UniProt NPD GO	ACT1_ABSGL	Actin-1 (Fragment)	0.00	-	cyt	0	Cytoplasm				140
P93376 UniProt NPD GO	ACT6_TOBAC	Actin-103 (Fragment)	0.00	-	cyt	0	Cytoplasm				336
P93375 UniProt NPD GO	ACT7_TOBAC	Actin-104 (Fragment)	0.00	-	cyt	0	Cytoplasm				336
Q96481 UniProt NPD GO	ACT4_LYCES	Actin-105 (Fragment)	0.00	-	cyt	0	Cytoplasm				336
P27132 UniProt NPD GO	ACT2_NAEFO	Actin-2 (Actin II) (Fragment)	0.00	-	cyt	0	Cytoplasm				371
P93587 UniProt NPD GO	ACT1_SOLTU	Actin-42 (Fragment)	0.00	-	cyt	0	Cytoplasm				332
P93586 UniProt NPD GO	ACT2_SOLTU	Actin-46 (Fragment)	0.00	-	cyt	0	Cytoplasm				336
Q96483 UniProt NPD GO	ACT2_LYCES	Actin-51 (Fragment)	0.00	-	cyt	0	Cytoplasm				336
P15986 UniProt NPD GO	ACT6_SOYBN	Actin-6 (Fragment)	0.00	-		0	Cytoplasm				17
P93372 UniProt NPD GO	ACT4_TOBAC	Actin-66 (Fragment)	0.00	-	cyt	0	Cytoplasm				336
P81228 UniProt NPD GO	ACT5_SOLTU	Actin-66 (Fragment)	0.00	-	cyt	0	Cytoplasm				336
P17300 UniProt NPD GO	ACT7_ORYSA	Actin-7	0.00	-	cyt	0	Cytoplasm	actin cytoskeleton [IEP] cytoplasm [IEP]			376
P15987 UniProt NPD GO	ACT7_SOYBN	Actin-7 (Fragment)	0.00	-		0	Cytoplasm				13
P81229 UniProt NPD GO	ACT8_SOLTU	Actin-79 (Fragment)	0.00	-	cyt	0	Cytoplasm				336
P30170 UniProt NPD GO	ACT10_SOLTU	Actin-85C (Fragment)	0.00	-	cyt	0	Cytoplasm				195
P80197 UniProt NPD GO	KAFK_PHYPO	Actin-fragmin kinase (EC 2.7.11.1) (AFK) (Fragments)	0.00	-	nuc	0	Cytoplasm				160
Q9WV32 UniProt NPD GO	ARC1B_MOUSE	Actin-related protein 2/3 complex subunit 1B (ARP2/3 complex 41 kDa subunit) (p41-ARC)	0.00	-	cyt	0		Arp2/3 protein complex [TAS]			371
Q3SYX9 UniProt NPD GO	ARPC5_BOVIN	Actin-related protein 2/3 complex subunit 5 (ARP2/3 complex 16 kDa subunit) (p16-ARC)	0.00	-	nuc	0					150
O15511 UniProt NPD GO	ARPC5_HUMAN	Actin-related protein 2/3 complex subunit 5 (ARP2/3 complex 16 kDa subunit) (p16-ARC)	0.00	-	nuc	0		Arp2/3 protein complex [TAS] cytoplasm [TAS]	604227		150
Q9CPW4 UniProt NPD GO	ARPC5_MOUSE	Actin-related protein 2/3 complex subunit 5 (ARP2/3 complex 16 kDa subunit) (p16-ARC)	0.00	-	nuc	0		Arp2/3 protein complex [TAS] lamellipodium [IDA]			150
Q5R516 UniProt NPD GO	ARPC5_PONPY	Actin-related protein 2/3 complex subunit 5 (ARP2/3 complex 16 kDa subunit) (p16-ARC)	0.00	-	nuc	0					150
Q8BK64 UniProt NPD GO	AHSA1_MOUSE	Activator of 90 kDa heat shock protein ATPase homolog 1 (AHA1)	0.00	-	nuc	0	Cytoplasm; cytosol (By similarity). Endoplasmic reticulum (By similarity). May transiently interact ...	cytoplasm [ISS]			338
O19921 UniProt NPD GO	ACP_CYACA	Acyl carrier protein (ACP)	0.00	-	cyt	0	Plastid; chloroplast				86
P51280 UniProt NPD GO	ACP_PORPU	Acyl carrier protein (ACP)	0.00	-	cyt	0	Plastid; chloroplast				84
P15543 UniProt NPD GO	ACP3_HORVU	Acyl carrier protein 3, chloroplast precursor (Acyl carrier protein III) (ACP III)	0.00	-	cyt	0	Plastid; chloroplast				132
Q9PRL8 UniProt NPD GO	ACBP_CHICK	Acyl-CoA-binding protein (ACBP) (Diazepam-binding inhibitor) (DBI)	0.00	-	cyt	0					86
P45882 UniProt NPD GO	ACBP_ANAPL	Acyl-CoA-binding protein (ACBP) (Diazepam-binding inhibitor) (DBI) (Endozepine) (EP)	0.00	-	cyt	0					103
Q8WN94 UniProt NPD GO	ACBP_RABIT	Acyl-CoA-binding protein (ACBP) (Diazepam-binding inhibitor) (DBI) (Endozepine) (EP)	0.00	-	cyt	0					86
P81624 UniProt NPD GO	ACBP1_DIGLA	Acyl-CoA-binding protein 1 (ACBP 1) (Fragment)	0.00	-	nuc	0	Cytoplasm				30
P81625 UniProt NPD GO	ACBP2_DIGLA	Acyl-CoA-binding protein 2 (ACBP 2) (Fragment)	0.00	-	nuc	0	Cytoplasm				40
P61868 UniProt NPD GO	ACBP2_SACMO	Acyl-CoA-binding protein 2 (ACBP type 2)	0.00	-	cyt	0					86
P61867 UniProt NPD GO	ACBP2_SACPS	Acyl-CoA-binding protein 2 (ACBP type 2)	0.00	-	cyt	0					86
P45883 UniProt NPD GO	ACBP_RANRI	Acyl-CoA-binding protein homolog (ACBP) (Diazepam-binding inhibitor homolog) (DBI)	0.00	-	cyt	0					87
O01805 UniProt NPD GO	ACBP1_CAEEL	Acyl-CoA-binding protein homolog 1 (ACBP-1) (Diazepam-binding inhibitor homolog) (DBI)	0.00	-	cyt	0					86
O55137 UniProt NPD GO	ACOT1_MOUSE	Acyl-coenzyme A thioesterase 1 (EC 3.1.2.2) (Acyl-CoA thioesterase 1) (Inducible cytosolic acyl-coen ...	0.00	-	mit	0	Cytoplasm	cytoplasm [TAS]			419
O88267 UniProt NPD GO	ACOT1_RAT	Acyl-coenzyme A thioesterase 1 (EC 3.1.2.2) (Acyl-CoA thioesterase 1) (Inducible cytosolic acyl-coen ...	0.00	-	mit	0	Cytoplasm	cytosol [IDA]			419
Q5AGD1 UniProt NPD GO	APTH1_CANAL	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.00	-	cyt	0	Cytoplasm (By similarity)				231
Q6BSS8 UniProt NPD GO	APTH1_DEBHA	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.00	-	mit	0	Cytoplasm (By similarity)				232
Q4PID3 UniProt NPD GO	APTH1_USTMA	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.00	-	mit	0	Cytoplasm (By similarity)				240
O95372 UniProt NPD GO	LYPA2_HUMAN	Acyl-protein thioesterase 2 (EC 3.1.2.-) (Lysophospholipase II) (LPL-I)	0.00	-	mit	0	Cytoplasm (Probable)				231
Q9QYL8 UniProt NPD GO	LYPA2_RAT	Acyl-protein thioesterase 2 (EC 3.1.2.-) (Lysophospholipase II) (Lysophospholipase 2)	0.00	-	mit	0	Cytoplasm (Probable)				231
Q9WTL7 UniProt NPD GO	LYPA2_MOUSE	Acyl-protein thioesterase 2 (EC 3.1.2.-) (Lysophospholipase II) (Lysophospholipase 2) (mLyso II)	0.00	-	mit	0	Cytoplasm (Probable)				231
P14620 UniProt NPD GO	ACYP2_ANAPL	Acylphosphatase-2 (EC 3.6.1.7) (Acylphosphate phosphohydrolase 2) (Acylphosphatase, muscle type isoz ...	0.00	-	cyt	0					102

You are viewing entries 92451 to 92500 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.